HAL3_ORYSJ
ID HAL3_ORYSJ Reviewed; 220 AA.
AC Q69K55; A0A0P0WU76;
DT 11-JUN-2014, integrated into UniProtKB/Swiss-Prot.
DT 13-SEP-2004, sequence version 1.
DT 03-AUG-2022, entry version 112.
DE RecName: Full=Phosphopantothenoylcysteine decarboxylase {ECO:0000303|PubMed:19232050};
DE Short=PPCDC {ECO:0000303|PubMed:19232050};
DE EC=4.1.1.36 {ECO:0000269|PubMed:19543273};
DE AltName: Full=Halotolerance protein HAL3 {ECO:0000303|PubMed:19232050};
DE Short=OsHAL3 {ECO:0000303|PubMed:19232050};
GN Name=HAL3 {ECO:0000303|PubMed:19232050};
GN OrderedLocusNames=Os06g0199500 {ECO:0000312|EMBL:BAS96646.1},
GN LOC_Os06g09910 {ECO:0000305};
GN ORFNames=B1172G12.27-1 {ECO:0000312|EMBL:BAD36646.1},
GN OJ1147_D11.5-1 {ECO:0000312|EMBL:BAD35576.1},
GN OsJ_20467 {ECO:0000312|EMBL:EEE65262.1};
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
RN [6]
RP FUNCTION, ACTIVE SITE, AND MUTAGENESIS OF MET-146; CYS-176; ASP-178 AND
RP GLY-180.
RX PubMed=19232050; DOI=10.1134/s000629790901009x;
RA Zhang N., Wang X., Chen J.;
RT "Role of OsHAL3 protein, a putative 4'-phosphopantothenoylcysteine
RT decarboxylase in rice.";
RL Biochemistry (Mosc.) 74:61-67(2009).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ACTIVE SITE, SUBUNIT, INTERACTION
RP WITH HIP1, TISSUE SPECIFICITY, INDUCTION, AND MUTAGENESIS OF
RP 107-SER--TYR-110 AND CYS-176.
RX PubMed=19543273; DOI=10.1038/ncb1892;
RA Sun S.Y., Chao D.Y., Li X.M., Shi M., Gao J.P., Zhu M.Z., Yang H.Q.,
RA Luan S., Lin H.X.;
RT "OsHAL3 mediates a new pathway in the light-regulated growth of rice.";
RL Nat. Cell Biol. 11:845-851(2009).
RN [8]
RP FUNCTION, INTERACTION WITH HD1, AND SUBCELLULAR LOCATION.
RX PubMed=26537047; DOI=10.1016/j.molp.2015.10.009;
RA Su L., Shan J.X., Gao J.P., Lin H.X.;
RT "OsHAL3, a blue light-responsive protein, interacts with the floral
RT regulator Hd1 to activate flowering in rice.";
RL Mol. Plant 9:233-244(2016).
CC -!- FUNCTION: Catalyzes the decarboxylation of 4'-
CC phosphopantothenoylcysteine to 4'-phosphopantetheine, a key step in
CC coenzyme A biosynthesis (PubMed:19232050, PubMed:19543273). Involved in
CC salt and osmotic tolerance, and light-regulated plant growth
CC (PubMed:19543273). Trimerization of HAL3 recruits and activates the E3
CC ubiquitin-protein ligase HIP1, which leads to the degradation of cell
CC cycle suppressors, resulting in enhancement of cell division and plant
CC growth (PubMed:19543273). HAL3 function in cell division seems to be
CC independent from its PPC decarboxylase activity (PubMed:19543273). Acts
CC as a positive regulator of flowering by binding to HD1 in the dark
CC (PubMed:26537047). {ECO:0000269|PubMed:19232050,
CC ECO:0000269|PubMed:19543273, ECO:0000269|PubMed:26537047}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H(+) + N-[(R)-4-phosphopantothenoyl]-L-cysteine = (R)-4'-
CC phosphopantetheine + CO2; Xref=Rhea:RHEA:16793, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16526, ChEBI:CHEBI:59458, ChEBI:CHEBI:61723; EC=4.1.1.36;
CC Evidence={ECO:0000269|PubMed:19543273};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:16794;
CC Evidence={ECO:0000269|PubMed:19543273};
CC -!- COFACTOR:
CC Name=FMN; Xref=ChEBI:CHEBI:58210;
CC Evidence={ECO:0000305|PubMed:19543273};
CC Note=Binds 1 FMN per subunit. {ECO:0000305|PubMed:19543273};
CC -!- PATHWAY: Cofactor biosynthesis; coenzyme A biosynthesis; CoA from (R)-
CC pantothenate: step 3/5. {ECO:0000305}.
CC -!- SUBUNIT: Forms homotrimers (PubMed:19543273). Interacts with HIP1
CC (PubMed:19543273). Interacts with HD1 in the dark (PubMed:26537047).
CC {ECO:0000269|PubMed:19543273, ECO:0000269|PubMed:26537047}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:26537047}.
CC -!- TISSUE SPECIFICITY: Expressed in root meristem, shoot apical meristem
CC (SAM), intercalary meristem, floral meristem, embryo and tip of the
CC coleoptile before true leaf emergence. {ECO:0000269|PubMed:19543273}.
CC -!- INDUCTION: Induced by dark. {ECO:0000269|PubMed:19543273}.
CC -!- MISCELLANEOUS: Seedlings over-expressing HAL3 show enhanced growth rate
CC under normal light/dark cycles, enhanced salt tolerance and Na(+)/K(+)
CC homeostasis. Enhanced growth is due to increased cell number of root
CC meristematic zone and root cap (PubMed:19543273).
CC {ECO:0000305|PubMed:19543273}.
CC -!- SIMILARITY: Belongs to the HFCD (homooligomeric flavin containing Cys
CC decarboxylase) superfamily. {ECO:0000305}.
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DR EMBL; AP003946; BAD35576.1; -; Genomic_DNA.
DR EMBL; AP006056; BAD36646.1; -; Genomic_DNA.
DR EMBL; AP008212; BAF18982.1; -; Genomic_DNA.
DR EMBL; AP014962; BAS96646.1; -; Genomic_DNA.
DR EMBL; CM000143; EEE65262.1; -; Genomic_DNA.
DR EMBL; AK060939; BAG87631.1; -; mRNA.
DR EMBL; AK064613; BAG89128.1; -; mRNA.
DR EMBL; AK100138; BAG94463.1; -; mRNA.
DR RefSeq; XP_015641201.1; XM_015785715.1.
DR RefSeq; XP_015641202.1; XM_015785716.1.
DR RefSeq; XP_015641203.1; XM_015785717.1.
DR AlphaFoldDB; Q69K55; -.
DR SMR; Q69K55; -.
DR STRING; 4530.OS06T0199500-02; -.
DR PaxDb; Q69K55; -.
DR PRIDE; Q69K55; -.
DR EnsemblPlants; Os06t0199500-01; Os06t0199500-01; Os06g0199500.
DR EnsemblPlants; Os06t0199500-02; Os06t0199500-02; Os06g0199500.
DR GeneID; 4340408; -.
DR Gramene; Os06t0199500-01; Os06t0199500-01; Os06g0199500.
DR Gramene; Os06t0199500-02; Os06t0199500-02; Os06g0199500.
DR KEGG; osa:4340408; -.
DR eggNOG; KOG0672; Eukaryota.
DR HOGENOM; CLU_033319_3_2_1; -.
DR InParanoid; Q69K55; -.
DR OMA; NTRMYDH; -.
DR OrthoDB; 1225808at2759; -.
DR UniPathway; UPA00241; UER00354.
DR Proteomes; UP000000763; Chromosome 6.
DR Proteomes; UP000007752; Chromosome 6.
DR Proteomes; UP000059680; Chromosome 6.
DR Genevisible; Q69K55; OS.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0071513; C:phosphopantothenoylcysteine decarboxylase complex; IBA:GO_Central.
DR GO; GO:0010181; F:FMN binding; IDA:UniProtKB.
DR GO; GO:0004633; F:phosphopantothenoylcysteine decarboxylase activity; IDA:UniProtKB.
DR GO; GO:0015937; P:coenzyme A biosynthetic process; IBA:GO_Central.
DR GO; GO:0070207; P:protein homotrimerization; IDA:UniProtKB.
DR GO; GO:0001558; P:regulation of cell growth; IMP:UniProtKB.
DR GO; GO:0009651; P:response to salt stress; IMP:UniProtKB.
DR Gene3D; 3.40.50.1950; -; 1.
DR InterPro; IPR036551; Flavin_trans-like.
DR InterPro; IPR003382; Flavoprotein.
DR Pfam; PF02441; Flavoprotein; 1.
DR SUPFAM; SSF52507; SSF52507; 1.
PE 1: Evidence at protein level;
KW Coenzyme A biosynthesis; Decarboxylase; Flavoprotein; FMN;
KW Growth regulation; Lyase; Nucleus; Reference proteome; Stress response.
FT CHAIN 1..220
FT /note="Phosphopantothenoylcysteine decarboxylase"
FT /id="PRO_0000429408"
FT ACT_SITE 91
FT /note="Proton donor"
FT /evidence="ECO:0000250|UniProtKB:Q9SWE5"
FT ACT_SITE 176
FT /note="Proton donor"
FT /evidence="ECO:0000305|PubMed:19232050,
FT ECO:0000305|PubMed:19543273"
FT BINDING 29..31
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250|UniProtKB:Q9SWE5"
FT BINDING 54..56
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250|UniProtKB:Q9SWE5"
FT BINDING 107..110
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250|UniProtKB:Q9SWE5"
FT BINDING 141
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250|UniProtKB:Q9SWE5"
FT BINDING 143
FT /ligand="N-[(R)-4-phosphopantothenoyl]-L-cysteine"
FT /ligand_id="ChEBI:CHEBI:59458"
FT /evidence="ECO:0000250|UniProtKB:Q9SWE5"
FT BINDING 173
FT /ligand="N-[(R)-4-phosphopantothenoyl]-L-cysteine"
FT /ligand_id="ChEBI:CHEBI:59458"
FT /evidence="ECO:0000250|UniProtKB:Q9SWE5"
FT BINDING 175
FT /ligand="N-[(R)-4-phosphopantothenoyl]-L-cysteine"
FT /ligand_id="ChEBI:CHEBI:59458"
FT /evidence="ECO:0000250|UniProtKB:Q9SWE5"
FT BINDING 184
FT /ligand="N-[(R)-4-phosphopantothenoyl]-L-cysteine"
FT /ligand_id="ChEBI:CHEBI:59458"
FT /evidence="ECO:0000250|UniProtKB:Q9SWE5"
FT SITE 176
FT /note="Important for catalytic activity"
FT /evidence="ECO:0000250|UniProtKB:Q9SWE5"
FT MUTAGEN 107..110
FT /note="SANT->PPYP: Loss of FMN binding and unable to form
FT homotrimer."
FT /evidence="ECO:0000269|PubMed:19543273"
FT MUTAGEN 146
FT /note="M->L: No effect on the activity."
FT /evidence="ECO:0000269|PubMed:19232050"
FT MUTAGEN 176
FT /note="C->S: Loss of activity."
FT /evidence="ECO:0000269|PubMed:19232050,
FT ECO:0000269|PubMed:19543273"
FT MUTAGEN 178
FT /note="D->N: No effect on the activity."
FT /evidence="ECO:0000269|PubMed:19232050"
FT MUTAGEN 180
FT /note="G->A: Reduces activity."
FT /evidence="ECO:0000269|PubMed:19232050"
SQ SEQUENCE 220 AA; 24084 MW; 10AB8B35D1D759F5 CRC64;
MTTSESVQET LGLDFPHPSK PRVLLAASGS VAAIKFESLC RSFSEWAEVR AVATKASLHF
IDRTSLPSNI ILYTDDDEWS TWKKIGDEVL HIELRKWADI MVIAPLSANT LAKIAGGLCD
NLLTCIVRAW DYSKPLFVAP AMNTFMWNNP FTSRHLETIN LLGISLVPPI TKRLACGDYG
NGAMAEPSVI DSTVRLACKR QPLNTNSSPV VPAGRNLPSS
